scRNA Seq Batch Summary: B002
Lauren Okada
2020-11-24
Batch Information
| Batch | B002 |
| N Samples | 24 |
| N Pools | 2 |
| B002-P1 Samples | IMM19_698, PB00004-01, PB00006-01, PB00010-01, PB00011-01, PB00012-01, PB00013-01, PB00014-01, PB00015-01, PB00016-01, PB00017-01, PB00018-01, PB00019-01 |
| B002-P2 Samples | IMM19_698, PB00020-01, PB00021-01, PB00022-01, PB00024-01, PB00053-01, PB00055-01, PB00056-01, PB00057-01, PB00059-01, PB00060-01, PB00061-01, PB00062-01 |
QC Results Summary
| Category | Results | Description |
|---|---|---|
| Well Sequencing and Alignment | Warning | |
| Cell Hashing | Pass | |
| Cell Labeling | Pass | |
| Control Sample | Pass |
Summary Details
Well Sequencing and Alignment
The following metrics summarize the sequencing and alignment by 10x well prior to un-hashing and hash-based cell filtering.
Detailed Well Summary
| Spec | Median_Range | Inter_Well_CV | Comments | Plot |
|---|---|---|---|---|
| estimated_number_of_cells | 27038 (21882-33097) | 11.2% | Fail: message | |
| fraction_reads_in_cells | 93.5 (92.1-94.9) | 0.9% | ||
| mean_reads_per_cell | 32890 (26087-43885) | 11.7% | ||
| median_genes_per_cell | 1594 (1500-1796) | 3.6% | Warning: message | |
| median_umi_counts_per_cell | 5309 (4848-6153) | 5.0% | ||
| number_of_reads | 920541389 (791967202-1088565134) | 6.9% | ||
| q30_bases_in_barcode | 95.6 (95.5-96.2) | 0.4% | ||
| q30_bases_in_rna_read | 93.8 (93.2-94.7) | 0.5% | ||
| q30_bases_in_sample_index | 93.7 (90.9-95.2) | 1.2% | ||
| q30_bases_in_umi | 95.4 (95.3-96.1) | 0.4% | ||
| reads_mapped_antisense_to_gene | 1.9 (1.7-2.1) | 5.9% | ||
| reads_mapped_confidently_to_exonic_regions | 64.8 (60.1-66.4) | 2.7% | ||
| reads_mapped_confidently_to_genome | 91.1 (88.3-92.4) | 1.2% | ||
| reads_mapped_confidently_to_intergenic_regions | 3.9 (3.8-4.2) | 2.8% | ||
| reads_mapped_confidently_to_intronic_regions | 22.7 (21.1-24.8) | 3.8% | Warning: message | |
| reads_mapped_confidently_to_transcriptome | 60.2 (55.4-62.1) | 3.1% | ||
| reads_mapped_to_genome | 95.3 (92.9-96.3) | 1.0% | ||
| sequencing_saturation | 64.4 (56.0-68.9) | 5.1% | Warning: message | |
| total_genes_detected | 24169 (23735-24554) | 1.1% | Warning: message | |
| valid_barcodes | 97.2 (97.0-97.4) | 0.1% |
Plots of Well-Level Metrics
Cell Hashing
| Specification | Value | Comments |
|---|---|---|
| x | x | |
| x | x | |
| x | x | Warning: message |
| x | x | Fail: mesage |
| x | x |
Singlet Summaries (hash-based)
HTO Barcode Count per Well Plot
##### HTO Barcode Fraction per Well Plot
Well Fraction per HTO Barcode Plot
Counts by HTO Category and Barcode
## Warning: Removed 2 rows containing non-finite values (stat_ydensity).
## Warning: Removed 3 rows containing non-finite values (stat_ydensity).## Warning: Removed 2 rows containing non-finite values (stat_ydensity).
Cell Labeling
| Specification | Value | Comments |
|---|---|---|
| x | x | |
| x | x | |
| x | x | Warning: message |
| x | x | Fail: mesage |
| x | x |
UMAP
## Warning: [ONE-TIME WARNING] Forked processing ('multicore') is disabled
## in future (>= 1.13.0) when running R from RStudio, because it is
## considered unstable. Because of this, plan("multicore") will fall
## back to plan("sequential"), and plan("multiprocess") will fall back to
## plan("multisession") - not plan("multicore") as in the past. For more details,
## how to control forked processing or not, and how to silence this warning in
## future R sessions, see ?future::supportsMulticore## Warning: Non-unique features (rownames) present in the input matrix, making
## unique## Centering and scaling data matrix## PC_ 1
## Positive: MNDA, FCN1, FGL2, CST3, CYBB, SERPINA1, CTSS, CSTA, NCF2, LYZ
## IGSF6, VCAN, S100A9, LST1, AIF1, PSAP, SPI1, TYROBP, CD68, MS4A6A
## CD14, TYMP, MPEG1, CPVL, S100A8, AC020656.1, GRN, CD302, CLEC12A, FCER1G
## Negative: IL7R, LTB, IL32, TRBC2, TRBC1, ISG20, HIST1H1D, SYNE2, MAL, GZMM
## HIST1H4C, RORA, AQP3, CTSW, SAMD3, CD69, CCL5, KLRB1, CD8B, GZMA
## ARID5B, PASK, GPR183, PYHIN1, CST7, FKBP11, AC013264.1, TSHZ2, CD8A, KLRG1
## PC_ 2
## Positive: CD79A, MS4A1, IGHM, BANK1, IGHD, TCL1A, RALGPS2, LINC00926, CD79B, HLA-DQA1
## TNFRSF13C, VPREB3, FCER2, HLA-DQB1, IGKC, FCRL1, LINC02397, AFF3, HLA-DRA, SPIB
## BCL11A, CD22, MEF2C, SWAP70, FAM129C, HLA-DRB1, FCRLA, GNG7, COBLL1, HVCN1
## Negative: NKG7, CST7, GZMA, KLRD1, CTSW, PRF1, CCL5, FGFBP2, HOPX, GZMM
## GNLY, CCL4, KLRF1, GZMB, TRDC, MATK, SPON2, S100A4, SAMD3, EFHD2
## GZMH, KLRB1, CLIC3, IL2RB, IFITM2, ANXA1, SRGN, FCGR3A, PTGDR, XCL2
## PC_ 3
## Positive: IL7R, MAL, TSHZ2, ADTRP, VIM, AQP3, VCAN, S100A8, PASK, LRRN3
## S100A12, LTB, S100A9, CSF3R, CD14, AIF1, CD4, LYZ, FCN1, AC013264.1
## AC020656.1, SLC40A1, IL17RA, PLBD1, CD36, CYP1B1, RBP7, MNDA, LINC02446, FPR1
## Negative: GZMB, NKG7, CST7, KLRD1, GZMA, CLIC3, PRF1, FGFBP2, KLRF1, HOPX
## GNLY, CCL4, CXXC5, PLEK, SPON2, CLIC1, CD79A, FCGR3A, MS4A1, CTSW
## CD79B, IGHM, CYBA, GZMH, BANK1, TRDC, APOBEC3G, MATK, PLAC8, CCL5
## PC_ 4
## Positive: MS4A1, IGHD, CD79A, LINC00926, JUN, RALGPS2, FCER2, CD79B, FCRL1, TNFRSF13C
## VPREB3, MT-CO1, IGHM, LINC02397, CD22, KLRD1, TCL1A, IER2, CYBA, ZFP36L1
## ADAM28, NEAT1, GZMA, PLPP5, SWAP70, NKG7, PAX5, CST7, IL4R, PRF1
## Negative: CAVIN2, TUBB1, PPBP, GNG11, PRKAR2B, PF4, CLU, GP9, NRGN, PTCRA
## ACRBP, HIST1H2AC, TREML1, MTURN, CMTM5, C2orf88, TSC22D1, SPARC, TMEM40, RGS18
## F13A1, MMD, MAP3K7CL, MYL9, RAB27B, RUFY1, HIST1H3H, HIST1H2BJ, CD9, CA2
## PC_ 5
## Positive: SERPINF1, PLD4, LILRA4, IL3RA, CLEC4C, ITM2C, GAS6, TPM2, LRRC26, SMPD3
## DERL3, SCT, DNASE1L3, PPP1R14B, LAMP5, IRF7, UGCG, SCN9A, MAP1A, MZB1
## LINC00996, JCHAIN, CCDC50, VIM, AL096865.1, MYBL2, PACSIN1, AC097375.1, AC119428.2, TNFRSF21
## Negative: CAVIN2, PPBP, TUBB1, PF4, GNG11, NRGN, CLU, GP9, PDLIM1, MT-CO1
## PRKAR2B, MS4A1, ACRBP, TREML1, IGHD, HIST1H2AC, RAB27B, CMTM5, BANK1, SPARC
## LINC00926, F13A1, RGS18, C2orf88, CD79A, GNLY, MAP3K7CL, TMEM40, TSPAN33, MMD
## Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
## To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
## This message will be shown once per session## 00:12:14 UMAP embedding parameters a = 0.9922 b = 1.112## 00:12:14 Read 78210 rows and found 4 numeric columns## 00:12:14 Using Annoy for neighbor search, n_neighbors = 30## 00:12:14 Building Annoy index with metric = cosine, n_trees = 50## 0% 10 20 30 40 50 60 70 80 90 100%## [----|----|----|----|----|----|----|----|----|----|## **************************************************|
## 00:12:34 Writing NN index file to temp file /tmp/RtmpUK6jXS/file17813677ee29
## 00:12:34 Searching Annoy index using 1 thread, search_k = 3000
## 00:13:26 Annoy recall = 100%
## 00:13:27 Commencing smooth kNN distance calibration using 1 thread
## 00:13:34 Initializing from normalized Laplacian + noise
## 00:14:07 Commencing optimization for 200 epochs, with 2579154 positive edges
## 00:16:01 Optimization finished## [1] TRUEUMAP Cell Visualizations
Seurat Labeling Scores
## Warning: Removed 26 rows containing missing values (geom_bar).
Marker Visualization
Leukopak Control
| Specification | Value | Comments |
|---|---|---|
| x | x | |
| x | x | |
| x | x | Warning: message |
| x | x | Fail: mesage |
| x | x |
Session Information
Files Analyzed:
## [1] "B002-P1_IMM19-698_labeled.h5" "B002-P1_PB00004-01_labeled.h5"
## [3] "B002-P1_PB00006-01_labeled.h5" "B002-P1_PB00010-01_labeled.h5"
## [5] "B002-P1_PB00011-01_labeled.h5" "B002-P1_PB00012-01_labeled.h5"
## [7] "B002-P1_PB00013-01_labeled.h5" "B002-P1_PB00014-01_labeled.h5"
## [9] "B002-P1_PB00015-01_labeled.h5" "B002-P1_PB00016-01_labeled.h5"
## [11] "B002-P1_PB00017-01_labeled.h5" "B002-P1_PB00018-01_labeled.h5"
## [13] "B002-P1_PB00019-01_labeled.h5" "B002-P2_IMM19-698_labeled.h5"
## [15] "B002-P2_PB00020-01_labeled.h5" "B002-P2_PB00021-01_labeled.h5"
## [17] "B002-P2_PB00022-01_labeled.h5" "B002-P2_PB00024-01_labeled.h5"
## [19] "B002-P2_PB00053-01_labeled.h5" "B002-P2_PB00055-01_labeled.h5"
## [21] "B002-P2_PB00056-01_labeled.h5" "B002-P2_PB00057-01_labeled.h5"
## [23] "B002-P2_PB00059-01_labeled.h5" "B002-P2_PB00060-01_labeled.h5"
## [25] "B002-P2_PB00061-01_labeled.h5" "B002-P2_PB00062-01_labeled.h5"Session Info:
## R version 3.6.0 (2019-04-26)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 9 (stretch)
##
## Matrix products: default
## BLAS: /usr/lib/libblas/libblas.so.3.7.0
## LAPACK: /usr/lib/lapack/liblapack.so.3.7.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] future.apply_1.6.0 future_1.19.1 inflection_1.3.5 Seurat_3.2.2
## [5] tidyr_1.1.2 immutils_0.0.2 plotly_4.9.2.1 gt_0.2.2
## [9] cowplot_1.1.0 dplyr_1.0.2 ggplot2_3.3.2 HTOparser_1.0.12
## [13] H5weaver_1.0.17 rlang_0.4.8 Matrix_1.2-17 data.table_1.13.2
## [17] rhdf5_2.28.1
##
## loaded via a namespace (and not attached):
## [1] Rtsne_0.15 colorspace_1.4-1 deldir_0.1-29
## [4] ellipsis_0.3.1 ggridges_0.5.2 spatstat.data_1.4-3
## [7] farver_2.0.3 leiden_0.3.3 listenv_0.8.0
## [10] ggrepel_0.8.1 RSpectra_0.16-0 codetools_0.2-16
## [13] splines_3.6.0 knitr_1.28 polyclip_1.10-0
## [16] jsonlite_1.6.1 ica_1.0-2 cluster_2.0.8
## [19] png_0.1-7 uwot_0.1.8 shiny_1.5.0
## [22] sctransform_0.3.1 compiler_3.6.0 httr_1.4.1
## [25] backports_1.1.4 assertthat_0.2.1 fastmap_1.0.1
## [28] lazyeval_0.2.2 later_1.0.0 htmltools_0.5.0
## [31] tools_3.6.0 rsvd_1.0.3 igraph_1.2.4.1
## [34] gtable_0.3.0 glue_1.4.1 RANN_2.6.1
## [37] reshape2_1.4.3 rappdirs_0.3.1 Rcpp_1.0.1
## [40] spatstat_1.64-1 vctrs_0.3.4 nlme_3.1-139
## [43] crosstalk_1.1.0.1 lmtest_0.9-38 xfun_0.14
## [46] stringr_1.4.0 globals_0.13.1 mime_0.9
## [49] miniUI_0.1.1.1 lifecycle_0.2.0 irlba_2.3.3
## [52] goftest_1.2-2 MASS_7.3-51.3 zoo_1.8-8
## [55] scales_1.1.1 promises_1.1.0 spatstat.utils_1.17-0
## [58] parallel_3.6.0 RColorBrewer_1.1-2 yaml_2.2.1
## [61] reticulate_1.16 pbapply_1.4-3 gridExtra_2.3
## [64] sass_0.2.0 rpart_4.1-15 stringi_1.4.3
## [67] checkmate_2.0.0 commonmark_1.7 pkgconfig_2.0.2
## [70] matrixStats_0.54.0 evaluate_0.14 lattice_0.20-38
## [73] ROCR_1.0-11 purrr_0.3.4 tensor_1.5
## [76] Rhdf5lib_1.6.3 labeling_0.3 patchwork_1.0.1
## [79] htmlwidgets_1.5.1 tidyselect_1.1.0 RcppAnnoy_0.0.16
## [82] plyr_1.8.4 magrittr_1.5 R6_2.4.0
## [85] generics_0.0.2 pillar_1.4.6 withr_2.1.2
## [88] mgcv_1.8-28 fitdistrplus_1.1-1 survival_2.44-1.1
## [91] abind_1.4-5 tibble_3.0.4 crayon_1.3.4
## [94] KernSmooth_2.23-15 rmarkdown_2.4 grid_3.6.0
## [97] digest_0.6.25 xtable_1.8-4 httpuv_1.5.4
## [100] munsell_0.5.0 viridisLite_0.3.0Total time elapsed
## [1] "Elapsed Time: 9.989 mins"